PUTRAJAYA, Malaysia, May 30 — In a controversial victory for Islamic law over secularism, Malaysia’s highest court today refused to recognize the conversion of a Muslim-born woman to Christianity, ruling that the matter was beyond the jurisdiction of the country’s civil courts and should be handled by religious authorities.

Muslims, who make up about 60 percent of Malaysia’s population, have co-existed with Buddhists, Christians, Hindus and Sikhs for decades in this country, considered one of the world’s most progressive and modern Muslim democracies.

But the ruling here underlined the increasing separateness of Muslims from people of other religions and reinforced the notion, widely held in many Muslim countries, that Islamic law should have primacy over secular laws in certain aspects of their lives.

The Federal Court was divided 2-1 in its decision, with the only non-Muslim judge, Richard Malanjum, dissenting forcefully and arguing that the Constitution must remain the supreme law of the land.

The ruling exhausted the last appeal of Lina Joy, who, after being baptized a Roman Catholic in May 1998, wanted to remove the word “Islam” from her identity card in order to marry her Catholic fiancé.

Muslims in Malaysia are subject to separate laws on inheritance and marriage — they must marry within the faith — and are not allowed to have premarital relationships or drink alcohol, among other rules.

Because separate laws apply to them, Muslims must list their religion on their identity cards.

Ms. Joy, who lost her job as a saleswoman last year because of the controversy and whose family has reportedly been harassed, is seeking political asylum in Australia, according to one of her advisers, who spoke on condition of anonymity because he was not authorized to speak for her.

Ms. Joy’s lawyer, Benjamin Dawson, was not available after the trial to comment on the verdict or the reported asylum application. Ms. Joy was not in the courtroom today.

The Malaysian chief justice, Ahmad Fairuz Abdul Halim, who read out his majority opinion in the packed but respectfully hushed courtroom, said the government agency responsible for identity cards had acted reasonably when it refused to change Ms. Joy’s religious status.

”She cannot at her own whim simply enter or leave her religion,” Mr. Ahmad said. “She must follow rules.”

The Malaysian Constitution is in some ways a self-contradicting document, analysts say.

It both defends freedom of religion and declares Islam the official religion. The abandonment of Islam, or apostasy, is deplored by many Muslims and in some Malaysian states is punishable by fines and imprisonment.

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Outside the courthouse, located in the heart of Malaysia’s gleaming administrative capital, jubilant members of an Islamic youth organization cheered the decision, shouting “Allah Akbar,” meaning “God is great.”

“We praise Allah for the position taken by the courts,” said Yusri Mohamad, the president of the Muslim Youth Movement of Malaysia. “We welcome and applaud the decision.”

But representatives of other religious communities said they were dismayed.

“Something needs to be done,” said Leonard Teoh Hooi Leong, a lawyer representing the Malaysia Consultative Council of Buddhism, Christianity, Hinduism and Sikhism. “People like Lina Joy should not be trapped in a legal cage.”

In practice, Mr. Teoh said, Ms. Joy, who was born Azlina Jailani, will have a very difficult time getting the Islamic authorities to allow her to leave Islam. No one in recent years has done it in the federal territory of Kuala Lumpur, where Ms. Joy is registered, he said. Those who have tried have been “threatened and cajoled,” Mr. Teoh said.

Ms. Joy’s case reflects the larger debate across the globe about the place of traditional Islamic beliefs in modern, multicultural democracies and highlights differences of opinion on the age-old question of the separation of religion and state.

”Islam in our country is not just a religion — it’s law,” said Pawancheek Marican, a Malaysian lawyer who attended the trial.

The specific Malaysian subtext of today’s decision is the system of legal and political segregation between Muslims and non-Muslims here that does not exist to the same extent in other multicultural countries with Muslim populations such as India or Indonesia.

Muslims in Malaysia are the main political power-brokers and the beneficiaries of a three-decade-old program of privileges for “bumiputra” — Malays and other indigenous people — who make up about 65 percent of the population and are mostly Muslims.

Large companies must respect hiring quotas for bumiputra as well as ownership rules that require certain levels of indigenous ownership.

But continued Malay political power is predicated on this thin majority of bumiputra, so the prospect of people like Lina Joy leaving Islam is disconcerting to the government.

These economic and political stakes add tension to the religious debate, with non-Muslims — mainly ethnic Chinese and Indians — resentful of the bumiputra’s privileges and power.

”For a long time I’ve noticed there has been an increase in Islamicization and discrimination,” Mr. Dawson, Ms. Joy’s lawyer, said in an interview last year.

Mr. Dawson, a Christian of mixed Chinese and Indian heritage and whose practice focuses mainly on commercial law, said he took up Ms. Joy’s case in 1999 as a sort of religious mission. “It was a calling, if you understand it from the Christian perspective,” he said.

He described Ms. Joy as “a simple and ordinary person” who felt strongly about her religious beliefs.